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FinalProjectPredict.m
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FinalProjectPredict.m
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(* ::Package:: *)
(* ::Title:: *)
(*Predicting Chemical Properties From Structure*)
(* ::Section:: *)
(*Prediction*)
(* ::Subsection::Closed:: *)
(*Melting Point*)
(* ::Input:: *)
(*fileLoc=NotebookDirectory[];*)
(*nFeat=250;*)
(*tempfile=StringJoin[fileLoc,"FinalSet.wl"];*)
(*Get[tempfile];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*Lset=Length[totalSet];*)
(**)
(*trainSet=totalSet[[1;;Round[0.7*Lset]]];*)
(*testSet=totalSet[[Round[0.7*Lset]+1;;Round[0.85*Lset]]];*)
(*validSet=totalSet[[Round[0.85*Lset]+1;;]];*)
(* ::Input:: *)
(*hashesTrain=Table[trainSet[[i]]["Hashes"],{i,1,Length[trainSet]}];*)
(*hashesTest=Table[testSet[[i]]["Hashes"],{i,1,Length[testSet]}];*)
(*hashesValid=Table[validSet[[i]]["Hashes"],{i,1,Length[validSet]}];*)
(**)
(*flatHashes=Flatten[DeleteDuplicates/@hashesTrain];*)
(*commonHashes=SortBy[Tally[flatHashes],-#[[2]]&];*)
(**)
(*(*featureList=#[[2]]&/@Select[commonHashes,#[[2]]>100&];*)*)
(*featureList=Commonest[flatHashes,nFeat];*)
(**)
(*groupsTrain=Table[Count[hashesTrain[[i]],featureList[[j]]],{i,1,Length[hashesTrain]},{j,1,Length[featureList]}];*)
(*groupsTest=Table[Count[hashesTest[[i]],featureList[[j]]],{i,1,Length[hashesTest]},{j,1,Length[featureList]}];*)
(*groupsValid=Table[Count[hashesValid[[i]],featureList[[j]]],{i,1,Length[hashesValid]},{j,1,Length[featureList]}];*)
(**)
(*atomTalliesTrain=Table[trainSet[[i]]["AtomTally"],{i,1,Length[trainSet]}];*)
(*atomTalliesTest=Table[testSet[[i]]["AtomTally"],{i,1,Length[testSet]}];*)
(*atomTalliesValid=Table[validSet[[i]]["AtomTally"],{i,1,Length[validSet]}];*)
(**)
(*allInputsTrain=Table[*)
(* Flatten[*)
(* {groupsTrain[[i]],*)
(* trainSet[[i]]["Cis"],*)
(* trainSet[[i]]["Trans"],*)
(* trainSet[[i]]["BondTally"],*)
(* trainSet[[i]]["TopoFeatures"],*)
(* trainSet[[i]]["Geom"],*)
(* Total[Abs[trainSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[trainSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* trainSet[[i]]["NetCharge"],*)
(* trainSet[[i]]["RotatableBondCount"],*)
(* trainSet[[i]]["HBondAcceptorCount"],*)
(* trainSet[[i]]["HBondDonorCount"],*)
(* trainSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]]/Total[atomTalliesTrain[[i]]],*)
(* atomTalliesTrain[[i]]}*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*allInputsTest=Table[*)
(* Flatten[*)
(* {groupsTest[[i]],*)
(* testSet[[i]]["Cis"],*)
(* testSet[[i]]["Trans"],*)
(* testSet[[i]]["BondTally"],*)
(* testSet[[i]]["TopoFeatures"],*)
(* testSet[[i]]["Geom"],*)
(* Total[Abs[testSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[testSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* testSet[[i]]["NetCharge"],*)
(* testSet[[i]]["RotatableBondCount"],*)
(* testSet[[i]]["HBondAcceptorCount"],*)
(* testSet[[i]]["HBondDonorCount"],*)
(* testSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]]/Total[atomTalliesTest[[i]]],*)
(* atomTalliesTest[[i]]}*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*allInputsValid=Table[*)
(* Flatten[*)
(* {groupsValid[[i]],*)
(* validSet[[i]]["Cis"],*)
(* validSet[[i]]["Trans"],*)
(* validSet[[i]]["BondTally"],*)
(* validSet[[i]]["TopoFeatures"],*)
(* validSet[[i]]["Geom"],*)
(* Total[Abs[validSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[validSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* validSet[[i]]["NetCharge"],*)
(* validSet[[i]]["RotatableBondCount"],*)
(* validSet[[i]]["HBondAcceptorCount"],*)
(* validSet[[i]]["HBondDonorCount"],*)
(* validSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]]/Total[atomTalliesValid[[i]]],*)
(* atomTalliesValid[[i]]}*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(**)
(**)
(*outputTrain=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* trainSet[[i]]["MeltingPoint"],*)
(* "Kelvins"*)
(* ]*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*outputTest=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* testSet[[i]]["MeltingPoint"],*)
(* "Kelvins"*)
(* ]*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*outputValid=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* validSet[[i]]["MeltingPoint"],*)
(* "Kelvins"*)
(* ]*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(* *)
(* *)
(* *)
(**)
(*trainData=Thread[allInputsTrain-> outputTrain];*)
(*testData=Thread[allInputsTest-> outputTest];*)
(*validData=Thread[allInputsValid-> outputValid];*)
(* ::Input:: *)
(*Clear[p];Clear[pm];p=Predict[trainData,ValidationSet->validData,FeatureTypes->"NumericalVector",PerformanceGoal->"Quality",Method->{"RandomForest","TreeNumber"-> 250,"LeafSize"->3}];*)
(* ::Input:: *)
(*pm=PredictorMeasurements[p,testData];*)
(*regressedData=p[allInputsTest];*)
(**)
(**)
(**)
(*meanPercentDiff=Mean[Abs[(regressedData-outputTest)/outputTest]]*100;*)
(*medDiff=Median[Abs[(regressedData-outputTest)]];*)
(**)
(*{pm["StandardDeviation"],pm["MeanDeviation"],medDiff,meanPercentDiff}*)
(* ::Input:: *)
(*range=Max[Join[outputTest,regressedData]]-Min[Join[outputTest,regressedData]];*)
(*aMin=Min[Join[outputTest,regressedData]]-0.05*range;*)
(*aMax=Max[Join[outputTest,regressedData]]+0.05*range;*)
(**)
(*Show[*)
(*ListPlot[*)
(*Table[*)
(*Tooltip[*)
(*{regressedData[[i]],outputTest[[i]]},*)
(*Column[*)
(*{*)
(*Keys[testSet][[i]],*)
(*Row[{"Predicted: " ,regressedData[[i]]," K"}],*)
(*Row[{"Actual: ",outputTest[[i]]," K"}]*)
(*}*)
(*]*)
(*],*)
(*{i,1,Length[testSet]}],*)
(*PlotRange->{{aMin,aMax},{aMin,aMax}},*)
(*AspectRatio->1,*)
(*AxesLabel->{"Predicted Value","Actual Value"},*)
(*LabelStyle->Large,*)
(*GridLines->Automatic*)
(*],*)
(*Graphics[{Dashed,Red,Line[{{aMin,aMin},{aMax,aMax}}]}]*)
(*]*)
(**)
(*pm["ResidualHistogram"]*)
(* ::Subsection::Closed:: *)
(*Boiling Point*)
(* ::Input:: *)
(*fileLoc=NotebookDirectory[];*)
(*nFeat=250;*)
(*tempfile=StringJoin[fileLoc,"FinalSet.wl"];*)
(*Get[tempfile];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(*Lset=Length[totalSet];*)
(**)
(*trainSet=totalSet[[1;;Round[0.7*Lset]]];*)
(*testSet=totalSet[[Round[0.7*Lset]+1;;Round[0.85*Lset]]];*)
(*validSet=totalSet[[Round[0.85*Lset]+1;;]];*)
(* ::Input:: *)
(*hashesTrain=Table[trainSet[[i]]["Hashes"],{i,1,Length[trainSet]}];*)
(*hashesTest=Table[testSet[[i]]["Hashes"],{i,1,Length[testSet]}];*)
(*hashesValid=Table[validSet[[i]]["Hashes"],{i,1,Length[validSet]}];*)
(**)
(*flatHashes=Flatten[DeleteDuplicates/@hashesTrain];*)
(*commonHashes=SortBy[Tally[flatHashes],-#[[2]]&];*)
(**)
(*(*featureList=#[[2]]&/@Select[commonHashes,#[[2]]>100&];*)*)
(*featureList=Commonest[flatHashes,nFeat];*)
(**)
(*groupsTrain=Table[Count[hashesTrain[[i]],featureList[[j]]],{i,1,Length[hashesTrain]},{j,1,Length[featureList]}];*)
(*groupsTest=Table[Count[hashesTest[[i]],featureList[[j]]],{i,1,Length[hashesTest]},{j,1,Length[featureList]}];*)
(*groupsValid=Table[Count[hashesValid[[i]],featureList[[j]]],{i,1,Length[hashesValid]},{j,1,Length[featureList]}];*)
(**)
(*atomTalliesTrain=Table[trainSet[[i]]["AtomTally"],{i,1,Length[trainSet]}];*)
(*atomTalliesTest=Table[testSet[[i]]["AtomTally"],{i,1,Length[testSet]}];*)
(*atomTalliesValid=Table[validSet[[i]]["AtomTally"],{i,1,Length[validSet]}];*)
(*allInputsTrain=Table[*)
(* Flatten[*)
(* {groupsTrain[[i]],*)
(* trainSet[[i]]["Cis"],*)
(* trainSet[[i]]["Trans"],*)
(* trainSet[[i]]["BondTally"],*)
(* trainSet[[i]]["TopoFeatures"],*)
(* trainSet[[i]]["Geom"],*)
(* Total[Abs[trainSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[trainSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* trainSet[[i]]["NetCharge"],*)
(* trainSet[[i]]["RotatableBondCount"],*)
(* trainSet[[i]]["HBondAcceptorCount"],*)
(* trainSet[[i]]["HBondDonorCount"],*)
(* trainSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]]/Total[atomTalliesTrain[[i]]],*)
(* atomTalliesTrain[[i]]}*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*allInputsTest=Table[*)
(* Flatten[*)
(* {groupsTest[[i]],*)
(* testSet[[i]]["Cis"],*)
(* testSet[[i]]["Trans"],*)
(* testSet[[i]]["BondTally"],*)
(* testSet[[i]]["TopoFeatures"],*)
(* testSet[[i]]["Geom"],*)
(* Total[Abs[testSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[testSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* testSet[[i]]["NetCharge"],*)
(* testSet[[i]]["RotatableBondCount"],*)
(* testSet[[i]]["HBondAcceptorCount"],*)
(* testSet[[i]]["HBondDonorCount"],*)
(* testSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]]/Total[atomTalliesTest[[i]]],*)
(* atomTalliesTest[[i]]}*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*allInputsValid=Table[*)
(* Flatten[*)
(* {groupsValid[[i]],*)
(* validSet[[i]]["Cis"],*)
(* validSet[[i]]["Trans"],*)
(* validSet[[i]]["BondTally"],*)
(* validSet[[i]]["TopoFeatures"],*)
(* validSet[[i]]["Geom"],*)
(* Total[Abs[validSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[validSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* validSet[[i]]["NetCharge"],*)
(* validSet[[i]]["RotatableBondCount"],*)
(* validSet[[i]]["HBondAcceptorCount"],*)
(* validSet[[i]]["HBondDonorCount"],*)
(* validSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]]/Total[atomTalliesValid[[i]]],*)
(* atomTalliesValid[[i]]}*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(**)
(**)
(*outputTrain=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* trainSet[[i]]["BoilingPoint"],*)
(* "Kelvins"*)
(* ]*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*outputTest=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* testSet[[i]]["BoilingPoint"],*)
(* "Kelvins"*)
(* ]*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*outputValid=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* validSet[[i]]["BoilingPoint"],*)
(* "Kelvins"*)
(* ]*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(* *)
(* *)
(* *)
(**)
(*trainData=Thread[allInputsTrain-> outputTrain];*)
(*testData=Thread[allInputsTest-> outputTest];*)
(*validData=Thread[allInputsValid-> outputValid];*)
(* ::Input:: *)
(*Clear[p];Clear[pm];p=Predict[trainData,ValidationSet->validData,FeatureTypes->"NumericalVector",PerformanceGoal->"Quality",Method->"RandomForest"];*)
(* ::Input:: *)
(*pm=PredictorMeasurements[p,testData];*)
(*regressedData=p[allInputsTest];*)
(**)
(**)
(**)
(*meanPercentDiff=Mean[Abs[(regressedData-outputTest)/outputTest]]*100;*)
(*medDiff=Median[Abs[(regressedData-outputTest)]];*)
(**)
(*{pm["StandardDeviation"],pm["MeanDeviation"],medDiff,meanPercentDiff}*)
(* ::Input:: *)
(*range=Max[Join[outputTest,regressedData]]-Min[Join[outputTest,regressedData]];*)
(*aMin=Min[Join[outputTest,regressedData]]-0.05*range;*)
(*aMax=Max[Join[outputTest,regressedData]]+0.05*range;*)
(**)
(*Show[*)
(*ListPlot[*)
(*Table[*)
(*Tooltip[*)
(*{regressedData[[i]],outputTest[[i]]},*)
(*Column[*)
(*{*)
(*Keys[testSet][[i]],*)
(*Row[{"Predicted: " ,regressedData[[i]]," K"}],*)
(*Row[{"Actual: ",outputTest[[i]]," K"}](*,*)
(*testSet[[i]]["BlackStructureDiagram"]*)*)
(*}*)
(*]*)
(*],*)
(*{i,1,Length[testSet]}],*)
(*PlotRange->{{aMin,aMax},{aMin,aMax}},*)
(*AspectRatio->1,*)
(*AxesLabel->{"Predicted Value","Actual Value"},*)
(*LabelStyle->Large*)
(*],*)
(*Graphics[{Dashed,Red,Line[{{aMin,aMin},{aMax,aMax}}]}]*)
(*]*)
(*pm["ResidualHistogram"]*)
(* ::Subsection::Closed:: *)
(*Heat of Fusion*)
(* ::Input:: *)
(*fileLoc=NotebookDirectory[];*)
(*nFeat=250;*)
(*tempfile=StringJoin[fileLoc,"FinalSet.wl"];*)
(*Get[tempfile];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*requiredProperties[A_]:=And[*)
(* Not[MissingQ[A["HeatFus"]]],*)
(* QuantityQ[A["HeatFus"]] *)
(* ]*)
(**)
(*totalSet=Select[totalSet,requiredProperties[#]&];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*Lset=Length[totalSet];*)
(**)
(*trainSet=totalSet[[1;;Round[0.7*Lset]]];*)
(*testSet=totalSet[[Round[0.7*Lset]+1;;Round[0.85*Lset]]];*)
(*validSet=totalSet[[Round[0.85*Lset]+1;;]];*)
(* ::Input:: *)
(*hashesTrain=Table[trainSet[[i]]["Hashes"],{i,1,Length[trainSet]}];*)
(*hashesTest=Table[testSet[[i]]["Hashes"],{i,1,Length[testSet]}];*)
(*hashesValid=Table[validSet[[i]]["Hashes"],{i,1,Length[validSet]}];*)
(**)
(*flatHashes=Flatten[DeleteDuplicates/@hashesTrain];*)
(*commonHashes=SortBy[Tally[flatHashes],-#[[2]]&];*)
(**)
(*(*featureList=#[[2]]&/@Select[commonHashes,#[[2]]>100&];*)*)
(*featureList=Commonest[flatHashes,nFeat];*)
(**)
(*groupsTrain=Table[Count[hashesTrain[[i]],featureList[[j]]],{i,1,Length[hashesTrain]},{j,1,Length[featureList]}];*)
(*groupsTest=Table[Count[hashesTest[[i]],featureList[[j]]],{i,1,Length[hashesTest]},{j,1,Length[featureList]}];*)
(*groupsValid=Table[Count[hashesValid[[i]],featureList[[j]]],{i,1,Length[hashesValid]},{j,1,Length[featureList]}];*)
(**)
(*atomTalliesTrain=Table[trainSet[[i]]["AtomTally"],{i,1,Length[trainSet]}];*)
(*atomTalliesTest=Table[testSet[[i]]["AtomTally"],{i,1,Length[testSet]}];*)
(*atomTalliesValid=Table[validSet[[i]]["AtomTally"],{i,1,Length[validSet]}];*)
(**)
(*allInputsTrain=Table[*)
(* Flatten[*)
(* {groupsTrain[[i]],*)
(* trainSet[[i]]["Cis"],*)
(* trainSet[[i]]["Trans"],*)
(* trainSet[[i]]["BondTally"],*)
(* trainSet[[i]]["TopoFeatures"],*)
(* trainSet[[i]]["Geom"],*)
(* Total[Abs[trainSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[trainSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* trainSet[[i]]["NetCharge"],*)
(* trainSet[[i]]["RotatableBondCount"],*)
(* trainSet[[i]]["HBondAcceptorCount"],*)
(* trainSet[[i]]["HBondDonorCount"],*)
(* trainSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]]/Total[atomTalliesTrain[[i]]],*)
(* atomTalliesTrain[[i]]}*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*allInputsTest=Table[*)
(* Flatten[*)
(* {groupsTest[[i]],*)
(* testSet[[i]]["Cis"],*)
(* testSet[[i]]["Trans"],*)
(* testSet[[i]]["BondTally"],*)
(* testSet[[i]]["TopoFeatures"],*)
(* testSet[[i]]["Geom"],*)
(* Total[Abs[testSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[testSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* testSet[[i]]["NetCharge"],*)
(* testSet[[i]]["RotatableBondCount"],*)
(* testSet[[i]]["HBondAcceptorCount"],*)
(* testSet[[i]]["HBondDonorCount"],*)
(* testSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]]/Total[atomTalliesTest[[i]]],*)
(* atomTalliesTest[[i]]}*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*allInputsValid=Table[*)
(* Flatten[*)
(* {groupsValid[[i]],*)
(* validSet[[i]]["Cis"],*)
(* validSet[[i]]["Trans"],*)
(* validSet[[i]]["BondTally"],*)
(* validSet[[i]]["TopoFeatures"],*)
(* validSet[[i]]["Geom"],*)
(* Total[Abs[validSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[validSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* validSet[[i]]["NetCharge"],*)
(* validSet[[i]]["RotatableBondCount"],*)
(* validSet[[i]]["HBondAcceptorCount"],*)
(* validSet[[i]]["HBondDonorCount"],*)
(* validSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]]/Total[atomTalliesValid[[i]]],*)
(* atomTalliesValid[[i]]}*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(**)
(**)
(*outputTrain=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* trainSet[[i]]["HeatFus"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*outputTest=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* testSet[[i]]["HeatFus"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*outputValid=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* validSet[[i]]["HeatFus"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(* *)
(* *)
(*trainData=Thread[allInputsTrain-> outputTrain];*)
(*testData=Thread[allInputsTest-> outputTest];*)
(*validData=Thread[allInputsValid-> outputValid];*)
(* ::Input:: *)
(*Clear[p];Clear[pm];p=Predict[trainData,ValidationSet->validData,FeatureTypes->"NumericalVector",PerformanceGoal->"Quality",Method->"RandomForest"];*)
(* ::Input:: *)
(*pm=PredictorMeasurements[p,testData];*)
(*regressedData=p[allInputsTest];*)
(**)
(**)
(**)
(*meanPercentDiff=Mean[Abs[(regressedData-outputTest)/outputTest]]*100;*)
(*medDiff=Median[Abs[(regressedData-outputTest)]];*)
(**)
(*{pm["StandardDeviation"],pm["MeanDeviation"],medDiff}*)
(* ::Input:: *)
(*range=Max[Join[outputTest,regressedData]]-Min[Join[outputTest,regressedData]];*)
(*aMin=Min[Join[outputTest,regressedData]]-0.05*range;*)
(*aMax=Max[Join[outputTest,regressedData]]+0.05*range;*)
(**)
(*Show[*)
(*ListPlot[*)
(*Table[*)
(*Tooltip[*)
(*{regressedData[[i]],outputTest[[i]]},*)
(*Column[*)
(*{*)
(*Keys[testSet][[i]],*)
(*Row[{"Predicted: " ,regressedData[[i]]," KJ/Mol"}],*)
(*Row[{"Actual: ",outputTest[[i]]," KJ/Mol"}](*,*)
(*testSet[[i]]["BlackStructureDiagram"]*)*)
(*}*)
(*]*)
(*],*)
(*{i,1,Length[testSet]}],*)
(*PlotRange->{{aMin,aMax},{aMin,aMax}},*)
(*AspectRatio->1,*)
(*AxesLabel->{"Predicted Value","Actual Value"},*)
(*LabelStyle->Large*)
(*],*)
(*Graphics[{Dashed,Red,Line[{{aMin,aMin},{aMax,aMax}}]}]*)
(*]*)
(*pm["ResidualHistogram"]*)
(* ::Subsection::Closed:: *)
(*Heat of Vaporization*)
(* ::Input:: *)
(*fileLoc=NotebookDirectory[];*)
(*nFeat=250;*)
(*tempfile=StringJoin[fileLoc,"FinalSet.wl"];*)
(*Get[tempfile];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*requiredProperties[A_]:=And[*)
(* Not[MissingQ[A["HeatVap"]]],*)
(* QuantityQ[A["HeatVap"]] *)
(* ]*)
(**)
(*totalSet=Select[totalSet,requiredProperties[#]&];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*Lset=Length[totalSet];*)
(**)
(*trainSet=totalSet[[1;;Round[0.7*Lset]]];*)
(*testSet=totalSet[[Round[0.7*Lset]+1;;Round[0.85*Lset]]];*)
(*validSet=totalSet[[Round[0.85*Lset]+1;;]];*)
(* ::Input:: *)
(*hashesTrain=Table[trainSet[[i]]["Hashes"],{i,1,Length[trainSet]}];*)
(*hashesTest=Table[testSet[[i]]["Hashes"],{i,1,Length[testSet]}];*)
(*hashesValid=Table[validSet[[i]]["Hashes"],{i,1,Length[validSet]}];*)
(**)
(*flatHashes=Flatten[DeleteDuplicates/@hashesTrain];*)
(*commonHashes=SortBy[Tally[flatHashes],-#[[2]]&];*)
(**)
(*(*featureList=#[[2]]&/@Select[commonHashes,#[[2]]>100&];*)*)
(*featureList=Commonest[flatHashes,nFeat];*)
(**)
(*groupsTrain=Table[Count[hashesTrain[[i]],featureList[[j]]],{i,1,Length[hashesTrain]},{j,1,Length[featureList]}];*)
(*groupsTest=Table[Count[hashesTest[[i]],featureList[[j]]],{i,1,Length[hashesTest]},{j,1,Length[featureList]}];*)
(*groupsValid=Table[Count[hashesValid[[i]],featureList[[j]]],{i,1,Length[hashesValid]},{j,1,Length[featureList]}];*)
(**)
(*atomTalliesTrain=Table[trainSet[[i]]["AtomTally"],{i,1,Length[trainSet]}];*)
(*atomTalliesTest=Table[testSet[[i]]["AtomTally"],{i,1,Length[testSet]}];*)
(*atomTalliesValid=Table[validSet[[i]]["AtomTally"],{i,1,Length[validSet]}];*)
(**)
(*allInputsTrain=Table[*)
(* Flatten[*)
(* {groupsTrain[[i]],*)
(* trainSet[[i]]["Cis"],*)
(* trainSet[[i]]["Trans"],*)
(* trainSet[[i]]["BondTally"],*)
(* trainSet[[i]]["TopoFeatures"],*)
(* trainSet[[i]]["Geom"],*)
(* Total[Abs[trainSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[trainSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* trainSet[[i]]["NetCharge"],*)
(* trainSet[[i]]["RotatableBondCount"],*)
(* trainSet[[i]]["HBondAcceptorCount"],*)
(* trainSet[[i]]["HBondDonorCount"],*)
(* trainSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]]/Total[atomTalliesTrain[[i]]],*)
(* atomTalliesTrain[[i]]}*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*allInputsTest=Table[*)
(* Flatten[*)
(* {groupsTest[[i]],*)
(* testSet[[i]]["Cis"],*)
(* testSet[[i]]["Trans"],*)
(* testSet[[i]]["BondTally"],*)
(* testSet[[i]]["TopoFeatures"],*)
(* testSet[[i]]["Geom"],*)
(* Total[Abs[testSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[testSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* testSet[[i]]["NetCharge"],*)
(* testSet[[i]]["RotatableBondCount"],*)
(* testSet[[i]]["HBondAcceptorCount"],*)
(* testSet[[i]]["HBondDonorCount"],*)
(* testSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]]/Total[atomTalliesTest[[i]]],*)
(* atomTalliesTest[[i]]}*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*allInputsValid=Table[*)
(* Flatten[*)
(* {groupsValid[[i]],*)
(* validSet[[i]]["Cis"],*)
(* validSet[[i]]["Trans"],*)
(* validSet[[i]]["BondTally"],*)
(* validSet[[i]]["TopoFeatures"],*)
(* validSet[[i]]["Geom"],*)
(* Total[Abs[validSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[validSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* validSet[[i]]["NetCharge"],*)
(* validSet[[i]]["RotatableBondCount"],*)
(* validSet[[i]]["HBondAcceptorCount"],*)
(* validSet[[i]]["HBondDonorCount"],*)
(* validSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]]/Total[atomTalliesValid[[i]]],*)
(* atomTalliesValid[[i]]}*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(**)
(**)
(*outputTrain=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* trainSet[[i]]["HeatVap"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*outputTest=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* testSet[[i]]["HeatVap"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*outputValid=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* validSet[[i]]["HeatVap"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(* *)
(* *)
(*trainData=Thread[allInputsTrain-> outputTrain];*)
(*testData=Thread[allInputsTest-> outputTest];*)
(*validData=Thread[allInputsValid-> outputValid];*)
(* ::Input:: *)
(*Clear[p];Clear[pm];p=Predict[trainData,ValidationSet->validData,FeatureTypes->"NumericalVector",PerformanceGoal->"Quality",Method->"RandomForest"];*)
(* ::Input:: *)
(*pm=PredictorMeasurements[p,testData];*)
(*regressedData=p[allInputsTest];*)
(**)
(**)
(**)
(*meanPercentDiff=Mean[Abs[(regressedData-outputTest)/outputTest]]*100;*)
(*medDiff=Median[Abs[(regressedData-outputTest)]];*)
(**)
(*{pm["StandardDeviation"],pm["MeanDeviation"],medDiff}*)
(* ::Input:: *)
(*range=Max[Join[outputTest,regressedData]]-Min[Join[outputTest,regressedData]];*)
(*aMin=Min[Join[outputTest,regressedData]]-0.05*range;*)
(*aMax=Max[Join[outputTest,regressedData]]+0.05*range;*)
(**)
(*Show[*)
(*ListPlot[*)
(*Table[*)
(*Tooltip[*)
(*{regressedData[[i]],outputTest[[i]]},*)
(*Column[*)
(*{*)
(*Keys[testSet][[i]],*)
(*Row[{"Predicted: " ,regressedData[[i]]," KJ/Mol"}],*)
(*Row[{"Actual: ",outputTest[[i]]," KJ/Mol"}](*,*)
(*testSet[[i]]["BlackStructureDiagram"]*)*)
(*}*)
(*]*)
(*],*)
(*{i,1,Length[testSet]}],*)
(*PlotRange->{{aMin,aMax},{aMin,aMax}},*)
(*AspectRatio->1,*)
(*AxesLabel->{"Predicted Value","Actual Value"},*)
(*PlotLabel->"Heat of Vaporization",*)
(*LabelStyle->Large*)
(*],*)
(*Graphics[{Dashed,Red,Line[{{aMin,aMin},{aMax,aMax}}]}]*)
(*]*)
(*pm["ResidualHistogram"]*)
(* ::Subsection::Closed:: *)
(*Heat of Combustion*)
(* ::Input:: *)
(*fileLoc=NotebookDirectory[];*)
(*nFeat=250;*)
(*tempfile=StringJoin[fileLoc,"FinalSet.wl"];*)
(*Get[tempfile];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*requiredProperties[A_]:=And[*)
(* Not[MissingQ[A["HeatComb"]]],*)
(* QuantityQ[A["HeatComb"]] *)
(* ]*)
(**)
(*totalSet=Select[totalSet,requiredProperties[#]&];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*Lset=Length[totalSet];*)
(**)
(*trainSet=totalSet[[1;;Round[0.7*Lset]]];*)
(*testSet=totalSet[[Round[0.7*Lset]+1;;Round[0.85*Lset]]];*)
(*validSet=totalSet[[Round[0.85*Lset]+1;;]];*)
(* ::Input:: *)
(*hashesTrain=Table[trainSet[[i]]["Hashes"],{i,1,Length[trainSet]}];*)
(*hashesTest=Table[testSet[[i]]["Hashes"],{i,1,Length[testSet]}];*)
(*hashesValid=Table[validSet[[i]]["Hashes"],{i,1,Length[validSet]}];*)
(**)
(*flatHashes=Flatten[DeleteDuplicates/@hashesTrain];*)
(*commonHashes=SortBy[Tally[flatHashes],-#[[2]]&];*)
(**)
(*(*featureList=#[[2]]&/@Select[commonHashes,#[[2]]>100&];*)*)
(*featureList=Commonest[flatHashes,nFeat];*)
(**)
(*groupsTrain=Table[Count[hashesTrain[[i]],featureList[[j]]],{i,1,Length[hashesTrain]},{j,1,Length[featureList]}];*)
(*groupsTest=Table[Count[hashesTest[[i]],featureList[[j]]],{i,1,Length[hashesTest]},{j,1,Length[featureList]}];*)
(*groupsValid=Table[Count[hashesValid[[i]],featureList[[j]]],{i,1,Length[hashesValid]},{j,1,Length[featureList]}];*)
(**)
(*atomTalliesTrain=Table[trainSet[[i]]["AtomTally"],{i,1,Length[trainSet]}];*)
(*atomTalliesTest=Table[testSet[[i]]["AtomTally"],{i,1,Length[testSet]}];*)
(*atomTalliesValid=Table[validSet[[i]]["AtomTally"],{i,1,Length[validSet]}];*)
(**)
(*allInputsTrain=Table[*)
(* Flatten[*)
(* {groupsTrain[[i]],*)
(* trainSet[[i]]["Cis"],*)
(* trainSet[[i]]["Trans"],*)
(* trainSet[[i]]["BondTally"],*)
(* trainSet[[i]]["TopoFeatures"],*)
(* trainSet[[i]]["Geom"],*)
(* Total[Abs[trainSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[trainSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* trainSet[[i]]["NetCharge"],*)
(* trainSet[[i]]["RotatableBondCount"],*)
(* trainSet[[i]]["HBondAcceptorCount"],*)
(* trainSet[[i]]["HBondDonorCount"],*)
(* trainSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[trainSet[[i]]["MolarMass"]]/Total[atomTalliesTrain[[i]]],*)
(* atomTalliesTrain[[i]]}*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*allInputsTest=Table[*)
(* Flatten[*)
(* {groupsTest[[i]],*)
(* testSet[[i]]["Cis"],*)
(* testSet[[i]]["Trans"],*)
(* testSet[[i]]["BondTally"],*)
(* testSet[[i]]["TopoFeatures"],*)
(* testSet[[i]]["Geom"],*)
(* Total[Abs[testSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[testSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* testSet[[i]]["NetCharge"],*)
(* testSet[[i]]["RotatableBondCount"],*)
(* testSet[[i]]["HBondAcceptorCount"],*)
(* testSet[[i]]["HBondDonorCount"],*)
(* testSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[testSet[[i]]["MolarMass"]]/Total[atomTalliesTest[[i]]],*)
(* atomTalliesTest[[i]]}*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*allInputsValid=Table[*)
(* Flatten[*)
(* {groupsValid[[i]],*)
(* validSet[[i]]["Cis"],*)
(* validSet[[i]]["Trans"],*)
(* validSet[[i]]["BondTally"],*)
(* validSet[[i]]["TopoFeatures"],*)
(* validSet[[i]]["Geom"],*)
(* Total[Abs[validSet[[i]]["FormalCharges"]]],*)
(* QuantityMagnitude[validSet[[i]]["TopologicalPolarSurfaceArea"]],*)
(* validSet[[i]]["NetCharge"],*)
(* validSet[[i]]["RotatableBondCount"],*)
(* validSet[[i]]["HBondAcceptorCount"],*)
(* validSet[[i]]["HBondDonorCount"],*)
(* validSet[[i]]["PrincipalMom"],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]],*)
(* QuantityMagnitude[validSet[[i]]["MolarMass"]]/Total[atomTalliesValid[[i]]],*)
(* atomTalliesValid[[i]]}*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(**)
(**)
(*outputTrain=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* trainSet[[i]]["HeatComb"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[trainSet]}];*)
(**)
(*outputTest=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* testSet[[i]]["HeatComb"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[testSet]}];*)
(* *)
(*outputValid=Table[*)
(* QuantityMagnitude[*)
(* UnitConvert[*)
(* validSet[[i]]["HeatComb"],*)
(* "Kilojoules"/"Moles"*)
(* ]*)
(* ],*)
(* {i,1,Length[validSet]}];*)
(* *)
(* *)
(*trainData=Thread[allInputsTrain-> outputTrain];*)
(*testData=Thread[allInputsTest-> outputTest];*)
(*validData=Thread[allInputsValid-> outputValid];*)
(* ::Input:: *)
(*Clear[p];Clear[pm];p=Predict[trainData,ValidationSet->validData,FeatureTypes->"NumericalVector",PerformanceGoal->"Quality",Method->"RandomForest"];*)
(* ::Input:: *)
(*pm=PredictorMeasurements[p,testData];*)
(*regressedData=p[allInputsTest];*)
(**)
(**)
(**)
(*meanPercentDiff=Mean[Abs[(regressedData-outputTest)/outputTest]]*100;*)
(*medDiff=Median[Abs[(regressedData-outputTest)]];*)
(**)
(*{pm["StandardDeviation"],pm["MeanDeviation"],medDiff}*)
(* ::Input:: *)
(*range=Max[Join[outputTest,regressedData]]-Min[Join[outputTest,regressedData]];*)
(*aMin=Min[Join[outputTest,regressedData]]-0.05*range;*)
(*aMax=Max[Join[outputTest,regressedData]]+0.05*range;*)
(**)
(*Show[*)
(*ListPlot[*)
(*Table[*)
(*Tooltip[*)
(*{regressedData[[i]],outputTest[[i]]},*)
(*Column[*)
(*{*)
(*Keys[testSet][[i]],*)
(*Row[{"Predicted: " ,regressedData[[i]]," KJ/Mol"}],*)
(*Row[{"Actual: ",outputTest[[i]]," KJ/Mol"}](*,*)
(*testSet[[i]]["BlackStructureDiagram"]*)*)
(*}*)
(*]*)
(*],*)
(*{i,1,Length[testSet]}],*)
(*PlotRange->{{aMin,aMax},{aMin,aMax}},*)
(*AspectRatio->1,*)
(*AxesLabel->{"Predicted Value","Actual Value"},*)
(*LabelStyle->Large*)
(*],*)
(*Graphics[{Dashed,Red,Line[{{aMin,aMin},{aMax,aMax}}]}]*)
(*]*)
(*pm["ResidualHistogram"]*)
(* ::Subsection::Closed:: *)
(*Heat of Formation*)
(* ::Input:: *)
(*fileLoc=NotebookDirectory[];*)
(*nFeat=250;*)
(*tempfile=StringJoin[fileLoc,"FinalSet.wl"];*)
(*Get[tempfile];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*requiredProperties[A_]:=And[*)
(* Not[MissingQ[A["HeatComb"]]],*)
(* QuantityQ[A["HeatComb"]], *)
(**)
(* Not[MissingQ[A["VertexTypes"]]],*)
(* SubsetQ[{"C","O","H"},DeleteDuplicates[A["VertexTypes"]]],*)
(* Length[DeleteDuplicates[A["VertexTypes"]]]>1,*)
(* SubsetQ[A["VertexTypes"],{"C"}]*)
(* *)
(* ]*)
(**)
(*totalSet=Select[totalSet,requiredProperties[#]&];*)
(*totalSet=RandomSample[totalSet,Length[totalSet]];*)
(**)
(*Lset=Length[totalSet];*)
(**)
(*trainSet=totalSet[[1;;Round[0.7*Lset]]];*)
(*testSet=totalSet[[Round[0.7*Lset]+1;;Round[0.85*Lset]]];*)
(*validSet=totalSet[[Round[0.85*Lset]+1;;]];*)
(* ::Input:: *)
(*heatH2O=-285.820;*)
(*heatCO2=-393.520;*)
(**)
(**)
(*hashesTrain=Table[trainSet[[i]]["Hashes"],{i,1,Length[trainSet]}];*)
(*hashesTest=Table[testSet[[i]]["Hashes"],{i,1,Length[testSet]}];*)
(*hashesValid=Table[validSet[[i]]["Hashes"],{i,1,Length[validSet]}];*)
(**)
(*flatHashes=Flatten[DeleteDuplicates/@hashesTrain];*)
(*commonHashes=SortBy[Tally[flatHashes],-#[[2]]&];*)
(**)
(*(*featureList=#[[2]]&/@Select[commonHashes,#[[2]]>100&];*)*)
(*featureList=Commonest[flatHashes,nFeat];*)
(**)
(*groupsTrain=Table[Count[hashesTrain[[i]],featureList[[j]]],{i,1,Length[hashesTrain]},{j,1,Length[featureList]}];*)
(*groupsTest=Table[Count[hashesTest[[i]],featureList[[j]]],{i,1,Length[hashesTest]},{j,1,Length[featureList]}];*)
(*groupsValid=Table[Count[hashesValid[[i]],featureList[[j]]],{i,1,Length[hashesValid]},{j,1,Length[featureList]}];*)
(**)
(*atomTalliesTrain=Table[trainSet[[i]]["AtomTally"],{i,1,Length[trainSet]}];*)
(*atomTalliesTest=Table[testSet[[i]]["AtomTally"],{i,1,Length[testSet]}];*)
(*atomTalliesValid=Table[validSet[[i]]["AtomTally"],{i,1,Length[validSet]}];*)
(**)
(*allInputsTrain=Table[*)
(* Flatten[*)
(* {groupsTrain[[i]],*)
(* trainSet[[i]]["Cis"],*)
(* trainSet[[i]]["Trans"],*)
(* trainSet[[i]]["BondTally"],*)
(* trainSet[[i]]["TopoFeatures"],*)